Quantitative Fluorescence Microscopy and Image Deconvolution

Methods in Cell Biology

Volumn 81, Issue , 2007, Pages 447-465

  Swedlow, Jason R ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EVALUATION; FLUORESCENCE MICROSCOPY; IMAGE PROCESSING; METHODOLOGY; REVIEW; THEORETICAL MODEL;

EVALUATION STUDIES; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, FLUORESCENCE; MODELS, THEORETICAL;

EID: 34248525914     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(06)81021-6     Document Type: Review

References (49)

1. Agard D.A. Optical sectioning microscopy: Cellular architecture in three dimensions. Ann. Rev. Biophys. Bioeng. 13 (1984) 191-219
2. Agard D.A., Hiraoka Y., Shaw P., and Sedat J.W. Fluorescence microscopy in three dimensions. Methods Cell Biol. 30 (1989) 353-377
3. Art J. Photon detectors for confocal microscopy. In: Pawley J.B. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum, New York 183-196
4. Boes M., Cerny J., Massol R., Op den Brouw M., Kirchhausen T., Chen J., and Ploegh H.L. T-cell engagement of dendritic cells rapidly rearranges MHC class II transport. Nature 418 (2002) 983-988
5. Bracewell R.N. "The Fourier Transform and its Applications." (1986), McGraw-Hill, New York
6. Carrington W. Image restoration in 3D microscopy with limited data. Proc. SPIE (Int. Soc. Optical Eng.) 1205 (1990) 72-83
7. Carrington W.A., Lynch R.M., Moore E.D., Isenberg G., Fogarty K.E., and Fay F.S. Superresolution three-dimensional images of fluorescence in cells with minimal light exposure. Science 268 (1995) 1483-1487
8. Chalfie M., Tu Y., Euskirchen G., Ward W.W., and Prasher D.C. Green fluorescent protein as a marker for gene expression. Science 263 (1994) 802-805
9. Chen H., Swedlow J.R., Grote M., Sedat J.W., and Agard D.A. The collection, processing, and display of digital three-dimensional images of biological specimens. In: Pawley J. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum Press, New York 197-210
10. Conchello J.A. Superresolution and convergence properties of the expectation-maximization algorithm for maximum-likelihood deconvolution of incoherent images. J. Opt. Soc. Am. A. 15 (1998) 2609-2619
11. Denk W., and Svoboda K. Photon upmanship: Why multiphoton imaging is more than a gimmick. Neuron 18 (1997) 351-357
12. Dernburg A.F., Broman K.W., Fung J.C., Marshall W.F., Philips J., Agard D.A., and Sedat J.W. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85 (1996) 745-759
13. Femino A.M., Fay F.S., Fogarty K., and Singer R.H. Visualization of single RNA transcripts in situ. Science 280 (1998) 585-590
14. Gibson S.F., and Lanni F. Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. J. Op. Soc. Am. 8 (1991) 1601-1613
15. Gold R. "An Iterative Unfolding Method for Response Matrices.". Argonne National Laboratory (1964) ANL-6984
16. Goodman J.W. "Introduction to Fourier Optics." (1996), McGraw-Hill, New York
17. Highett M.I., Beven A.F., and Shaw P.J. Localization of 5 S genes and transcripts in Pisum sativum nuclei. J. Cell Sci. 105 (1993) 1151-1158
18. Holmes T.J. Blind deconvolution of quantum-limited imagery: Maximum likelihood approach. J. Opt. Soc. Am. A. 9 (1992) 1052-1061
19. Holmes T.J., Bhattacharya S., Cooper J.A., Hanzel D., Krishnamurthi V., Lin W.-C., Roysam B., Szarowski D.H., and Turner J.N. Light microscopic images reconstructed by maximum likelihood deconvolution. In: Pawley J. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum Press, New York 389-402
20. Inoué S. Foundations of confocal scanned imaging in light microscopy. In: Pawley J. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum Press, New York 1-17
21. Inoue S., and Inoué T. Direct-view high-speed confocal scanner: The CSU-10. Methods Cell Biol. 70 (2002) 87-127
22. Inoué S., and Spring K.R. "Video Microscopy" (1997), Plenum Press, New York
23. Kam Z., Hanser B., Gustafsson M.G.L., Agard D.A., and Sedat J.W. Computational adaptive optics for live three-dimensional biological imaging. Proc. Natl. Acad. Sci. USA 98 (2001) 3790-3795
24. Lippincott-Schwartz J., Snapp E., and Kenworthy A. Studying protein dynamics in living cells. Nat. Rev. Mol. Cell Biol. 2 (2001) 444-456
25. Maddox P.S., Moree B., Canman J.C., and Salmon E.D. A spinning disk confocal microscope system for rapid high resolution, multimode, fluorescence speckle microscopy and GFP imaging in living cells. Methods Enzymol. 360 (2002) 597-617
26. McNally J.G., Karpova T., Cooper J., and Conchello J.A. Three-dimensional imaging by deconvolution microscopy. Methods 19 (1999) 373-385
27. Monks C.R., Freiberg B.A., Kupfer H., Sciaky N., and Kupfer A. Three-dimensional segregation of supramolecular activation clusters in T cells. Nature 395 (1998) 82-86
28. Murray J.M. Evaluating the performance of fluorescence microscopes. J. Microsc. 191 (1998) 128-134
29. Patterson G., Day R.N., and Piston D. Fluorescent protein spectra. J. Cell Sci. 114 (2001) 837-838
30. Pawley J. Fundamental limits in confocal microscopy. In: Pawley J. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum Press, New York 19-37
31. Pawley J. "Handbook of Confocal Microscopy,". 2nd Ed (1995), Plenum Press, New York
32. Pawley J.B. The sources of noise in three-dimensional data sets. In: Stevens J. (Ed). "Three Dimensional Confocal Microscopy" (1994), Academic Press, New York 47-94
33. Platani M., Goldberg I., Lamond A.I., and Swedlow J.R. Cajal body dynamics and association with chromatin are ATP-dependent. Nature Cell Biol. 4 (2002) 502-508
34. Russ J.C. "The Image Processing Handbook." (1992), CRC Press, Boca Raton, FL
35. Schaefer L.H., Schuster D., and Herz H. Generalized approach for accelerated maximum likelihood based image restoration applied to three-dimensional fluorescence microscopy. J. Microsc. 204 (2001) 99-107
36. Shaw P.J. Computer reconstruction in three-dimensional fluorescence microscopy. In: Shotton D. (Ed). "Electronic Light Microscopy" (1993), Wiley-Liss, New York 211-230
37. Shaw P.J., and Rawlins D.J. The point-spread of a confocal microscope: Its measurement and use in deconvolution of 3-D data. J. Microsc. 163 (1991) 151-165
38. Sheppard C.J.R., Gan X., Gu M., and Roy M. Signal-to-noise in confocal microscopes. In: Pawley J.B. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum, New York 363-402
39. Silver R.B. Ratio imaging: Practical considerations for measuring intracellular calcium and pH in living tissue. Methods Cell Biol. 56 (1998) 237-251
40. Stearns T. Green fluorescent protein. The green revolution. Curr. Biol. 5 (1995) 262-264
41. Swedlow J.R., Hu K., Andrews P.D., Roos D.S., and Murray J.M. Measuring tubulin content in Toxoplasma gondii: A comparison of laser-scanning confocal and wide-field fluorescence microscopy. Proc. Soc. Natl. Acad. USA 99 (2002) 2014-2019
42. Swedlow J.R., and Platani M. Live cell imaging using wide-field microscopy and deconvolution. Cell Struct. Funct. 27 (2002) 335-341
43. Swedlow J.R., Sedat J.W., and Agard D.A. Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide field microscopy. Cell 73 (1993) 97-108
44. Swedlow J.R., Sedat J.W., and Agard D.A. Deconvolution in optical microscopy. In: Jansson P.A. (Ed). "Deconvolution of Images and Spectra" (1997), Academic Press, New York 284-309
45. Tsien R.Y. The green fluorescent protein. Annu. Rev. Biochem. 67 (1998) 509-544
46. Tsien R.Y., and Waggoner A. Fluorophores for confocal microscopy: Photophysics and photochemistry. In: Pawley J.B. (Ed). "Handbook of Biological Confocal Microscopy" (1995), Plenum, New York 267-280
47. Wallace W., Schaefer L.H., and Swedlow J.R. A working person's guide to deconvolution in light microscopy. Biotechniques 31 (2001) 1076-1097
48. Wilkie G.S., and Davis I. Drosophila wingless and pair-rule transcripts localize apically by dynein-mediated transport of RNA particles. Cell 105 (2001) 209-219
49. Zucker R.M., and Price O. Evaluation of confocal microscopy system performance. Cytometry 44 (2001) 273-294